Variant report

Variant	rs12440265
Chromosome Location	chr15:83726267-83726268
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:83725788-83727589	K562	blood:	n/a	n/a
2	POLR2A	chr15:83725711-83726898	GM12878	blood:	n/a	n/a
3	GATA1	chr15:83726234-83726829	PBDE	blood:	n/a	n/a
4	POLR2A	chr15:83726186-83727043	K562	blood:	n/a	n/a
5	USF1	chr15:83725795-83726287	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:83725462..83726984-chr15:83728887..83730792,2	MCF-7	breast:
2	chr15:83681090..83684205-chr15:83725354..83727714,3	K562	blood:
3	chr15:83723727..83726962-chr15:83733649..83736158,3	MCF-7	breast:

Variant related genes	Relation type
BTBD1	TF binding region
ENSG00000263643	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000249214	Chromatin interaction
ENSG00000260608	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1010820	0.94[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1045742	0.94[CEU][hapmap]
rs10520576	0.94[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs1075619	0.94[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112404	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs11259965	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs11259967	0.81[EUR][1000 genomes]
rs11259968	0.85[EUR][1000 genomes]
rs11259969	0.94[CEU][hapmap]
rs11259970	0.85[EUR][1000 genomes]
rs11852287	0.81[EUR][1000 genomes]
rs11852408	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs11852446	0.85[EUR][1000 genomes]
rs11852496	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11853498	0.94[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.84[EUR][1000 genomes]
rs11855639	0.84[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.85[EUR][1000 genomes]
rs11857428	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs11857641	1.00[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11857990	0.89[GIH][hapmap]
rs11858162	1.00[CEU][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	0.94[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11858468	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437558	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12437901	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.84[EUR][1000 genomes]
rs12438526	1.00[ASN][1000 genomes]
rs12438575	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438708	1.00[ASN][1000 genomes]
rs12439122	1.00[ASN][1000 genomes]
rs12439903	0.85[EUR][1000 genomes]
rs12440386	0.83[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12440562	0.94[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	0.94[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.85[EUR][1000 genomes]
rs12441907	1.00[ASN][1000 genomes]
rs12442894	0.94[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12443109	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12443424	0.85[EUR][1000 genomes]
rs12591855	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs12593532	0.84[EUR][1000 genomes]
rs12593638	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12595330	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs17359494	0.83[MEX][hapmap]
rs17361375	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.85[EUR][1000 genomes]
rs17507763	0.85[EUR][1000 genomes]
rs17508610	0.94[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	0.94[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs17567869	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs17568298	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1877024	1.00[ASN][1000 genomes]
rs1901544	0.81[EUR][1000 genomes]
rs2034618	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs41326445	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap]
rs4300612	1.00[ASN][1000 genomes]
rs4408505	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423388	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480763	1.00[ASN][1000 genomes]
rs4547301	1.00[ASN][1000 genomes]
rs4563011	0.94[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4572349	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683536	0.85[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55756182	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55878453	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893521	1.00[ASN][1000 genomes]
rs55905779	1.00[ASN][1000 genomes]
rs55932429	1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs56045305	0.84[EUR][1000 genomes]
rs56052029	0.84[EUR][1000 genomes]
rs56352317	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.85[EUR][1000 genomes]
rs57729044	0.85[EUR][1000 genomes]
rs58006707	0.85[EUR][1000 genomes]
rs58281154	0.85[EUR][1000 genomes]
rs58396076	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58847484	1.00[ASN][1000 genomes]
rs59828448	1.00[ASN][1000 genomes]
rs59896565	0.84[EUR][1000 genomes]
rs60344060	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267530	0.82[EUR][1000 genomes]
rs62010162	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010164	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010170	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010172	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010173	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.85[EUR][1000 genomes]
rs62010214	0.83[EUR][1000 genomes]
rs62010215	0.85[EUR][1000 genomes]
rs62010220	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.85[EUR][1000 genomes]
rs62010252	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.85[EUR][1000 genomes]
rs62010258	0.85[EUR][1000 genomes]
rs62011742	0.86[EUR][1000 genomes]
rs62011744	0.89[EUR][1000 genomes]
rs62011869	0.86[EUR][1000 genomes]
rs62025914	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025915	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025919	1.00[ASN][1000 genomes]
rs62025921	1.00[ASN][1000 genomes]
rs62025923	1.00[ASN][1000 genomes]
rs6603042	0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs66619192	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67022650	0.87[EUR][1000 genomes]
rs67933024	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164083	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7165114	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs7165978	0.94[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7166078	1.00[ASN][1000 genomes]
rs716886	0.84[GIH][hapmap]
rs7172590	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177462	0.84[GIH][hapmap]
rs7179675	1.00[ASN][1000 genomes]
rs7180692	1.00[ASN][1000 genomes]
rs7183171	1.00[ASN][1000 genomes]
rs72755992	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	0.94[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs8027577	0.94[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs8031723	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033380	1.00[ASN][1000 genomes]
rs8038486	0.94[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs8043224	0.94[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs965263	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs9707895	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:83708800-83726400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr15:83708800-83726600	Weak transcription	Pancreas	Pancrea
9	chr15:83709000-83726600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:83709000-83726600	Weak transcription	Fetal Brain Male	brain
11	chr15:83709200-83727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
15	chr15:83713600-83726600	Weak transcription	Gastric	stomach
16	chr15:83714200-83730200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:83714400-83726600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:83717000-83726400	Weak transcription	Small Intestine	intestine
19	chr15:83717000-83726800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:83717400-83731400	Weak transcription	Spleen	Spleen
21	chr15:83718000-83726600	Weak transcription	Aorta	Aorta
22	chr15:83718000-83731000	Weak transcription	Colonic Mucosa	Colon
23	chr15:83718400-83727800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:83719800-83726600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:83719800-83729800	Weak transcription	NHEK	skin
26	chr15:83720000-83729800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:83720400-83728600	Strong transcription	GM12878-XiMat	blood
28	chr15:83720800-83726400	Strong transcription	Fetal Muscle Leg	muscle
29	chr15:83720800-83728600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:83721200-83726800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr15:83721800-83726400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:83721800-83727000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:83721800-83727000	Strong transcription	Primary T cells from cord blood	blood
34	chr15:83722000-83726800	Strong transcription	K562	blood
35	chr15:83722000-83727200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:83722400-83727000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:83722400-83730200	Weak transcription	HSMMtube	muscle
38	chr15:83722600-83726800	Strong transcription	Fetal Intestine Large	intestine
39	chr15:83722600-83727000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:83722600-83730200	Weak transcription	NHDF-Ad	bronchial
41	chr15:83722600-83732800	Weak transcription	NHLF	lung
42	chr15:83722800-83726800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:83722800-83727000	Strong transcription	Fetal Stomach	stomach
44	chr15:83722800-83730200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:83723200-83726600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr15:83723200-83726600	Weak transcription	Psoas Muscle	Psoas
47	chr15:83723400-83729600	Weak transcription	Fetal Kidney	kidney
48	chr15:83723800-83729800	Weak transcription	HMEC	breast
49	chr15:83724000-83726600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:83724600-83727000	Strong transcription	Dnd41	blood

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